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Sibounheuang B, Boutthasavong L, Chommanam D, Phommasone K, Panapruksachat S, Praphasiri V, Bouttavong S, Sisavath H, Christy NCV, Letizia AG, Mayxay M, Vongsouvath M, Ashley EA, Dubot-Pérès A. Dry Swabs and Dried Saliva as Alternative Samples for SARS-CoV-2 Detection in Remote Areas in Lao PDR. Open Forum Infect Dis 2024; 11:ofae433. [PMID: 39145142 PMCID: PMC11322834 DOI: 10.1093/ofid/ofae433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 07/22/2024] [Indexed: 08/16/2024] Open
Abstract
Background Surveillance of SARS-CoV-2 circulation is mainly based on real-time reverse transcription-polymerase chain reaction, which requires laboratory facilities and cold chain for sample transportation. This is difficult to achieve in remote rural areas of resource-limited settings. The use of dried blood spots shipped at room temperature has shown good efficiency for the detection of arboviral RNA. Using a similar approach, we conducted a study at 3 provincial hospitals in Laos to compare the detection of SARS-CoV-2 from neat and dried spot samples. Methods Between January 2022 and March 2023, patients with respiratory symptoms were recruited. Nasopharyngeal/oropharyngeal swabs in virus transport medium (VTM), dry swabs, saliva, and dried saliva spotted on filter paper were collected. All samples were tested by SARS-CoV-2 real-time reverse transcription-polymerase chain reaction. Results In total, 479 participants were included. The VTM samples tested positive for 288 (60.1%). High positive percent agreements were observed for dry swab (84.8%; 95% CI, 80.2%-88.8%) and saliva (89.2%; 95% CI, 85.1%-92.6%) as compared with VTM. There was a loss of sensitivity when saliva was dried on filter paper (73.6%; 95% CI, 68.1%-78.6%) as compared with saliva. SARS-CoV-2 variant (Delta or Omicron) had no significant impact on the performance of the different sample types. Conclusions Our findings suggest that dry swabs could be a good alternative for sample collection and permit easy shipping at ambient temperature for subsequent viral SARS-CoV-2 RNA purification and molecular investigation. This is a useful tool to consider for a rapid implementation of large-scale surveillance of SARS-CoV-2 in remote areas, which could be extrapolated to other respiratory targets during routine surveillance or in the case of a novel emerging pandemic.
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Affiliation(s)
- Bountoy Sibounheuang
- Microbiology Laboratory, Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Mahosot Hospital, Vientiane, Lao PDR
| | - Latsaniphone Boutthasavong
- Microbiology Laboratory, Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Mahosot Hospital, Vientiane, Lao PDR
| | - Danoy Chommanam
- Microbiology Laboratory, Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Mahosot Hospital, Vientiane, Lao PDR
| | - Koukeo Phommasone
- Microbiology Laboratory, Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Mahosot Hospital, Vientiane, Lao PDR
| | - Siribun Panapruksachat
- Microbiology Laboratory, Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Mahosot Hospital, Vientiane, Lao PDR
| | | | | | | | - Nathaniel C V Christy
- Naval Medical Research Unit INDO PACIFIC, Emerging Infectious Disease Department, Singapore, Singapore
| | - Andrew G Letizia
- Naval Medical Research Unit INDO PACIFIC, Emerging Infectious Disease Department, Singapore, Singapore
| | - Mayfong Mayxay
- Microbiology Laboratory, Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Mahosot Hospital, Vientiane, Lao PDR
- Nuffield Department of Clinical Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Institute of Research and Education Development, University of Health Sciences, Vientiane, Lao PDR
| | - Manivanh Vongsouvath
- Microbiology Laboratory, Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Mahosot Hospital, Vientiane, Lao PDR
| | - Elizabeth A Ashley
- Microbiology Laboratory, Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Mahosot Hospital, Vientiane, Lao PDR
- Nuffield Department of Clinical Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Audrey Dubot-Pérès
- Microbiology Laboratory, Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Mahosot Hospital, Vientiane, Lao PDR
- Nuffield Department of Clinical Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
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2
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Saba Villarroel PM, Chaiphongpachara T, Nurtop E, Laojun S, Pangpoo-Nga T, Songhong T, Supungul D, Baronti C, Thirion L, Leaungwutiwong P, de Lamballerie X, Missé D, Wichit S. Seroprevalence study in humans and molecular detection in Rhipicephalus sanguineus ticks of severe fever with thrombocytopenia syndrome virus in Thailand. Sci Rep 2024; 14:13397. [PMID: 38862576 PMCID: PMC11167008 DOI: 10.1038/s41598-024-64242-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 06/06/2024] [Indexed: 06/13/2024] Open
Abstract
Severe fever with thrombocytopenia syndrome virus (SFTSV) is an emerging tick-borne virus with a mortality rate of up to 30%. First identified in China in 2009, it was later reported in other Asian countries, including Thailand in 2020. SFTSV has been detected in several tick species, including Rhipicephalus sanguineus, known for infesting dogs. We conducted a seroprevalence study of SFTSV in Bangkok and Nong Khai, Thailand, by analyzing 1162 human samples collected between 2019 and 2023. The testing method relied on IgG detection using ELISA and confirmed though a virus seroneutralization test. The results indicated that out of the participants, 12 (1.1%) tested positive for anti-SFTSV IgG antibodies; however, none exhibited positive results in the seroneutralization assay. Additionally, molecular detection of SFTSV, Crimean-Congo hemorrhagic fever (CCHF), Coxiella spp., Bartonella spp., and Rickettsia spp. was performed on 433 Rh. sanguineus ticks collected from 49 dogs in 2023 in Chachoengsao Province, Thailand. No evidence of these pathogens was found in ticks. These findings highlight the importance of exploring viral cross-reactivity. Furthermore, it is important to conduct additional studies to isolate SFTSV from animals and ticks in order to identify the potential transmission routes contributing to human and animal infections in Thailand.
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Affiliation(s)
- Paola Mariela Saba Villarroel
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, Thailand
- Viral Vector Joint Unit and Joint Laboratory, Mahidol University, Nakhon Pathom, Thailand
| | - Tanawat Chaiphongpachara
- Department of Public Health and Health Promotion, College of Allied Health Sciences, Suan Sunandha Rajabhat University, Samut Songkhram, Thailand
| | - Elif Nurtop
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190- Inserm 1207), Marseille, France
| | - Sedthapong Laojun
- Department of Public Health and Health Promotion, College of Allied Health Sciences, Suan Sunandha Rajabhat University, Samut Songkhram, Thailand
| | | | - Thanaphon Songhong
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, Thailand
- Viral Vector Joint Unit and Joint Laboratory, Mahidol University, Nakhon Pathom, Thailand
| | - Dolruethai Supungul
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, Thailand
- Viral Vector Joint Unit and Joint Laboratory, Mahidol University, Nakhon Pathom, Thailand
| | - Cécile Baronti
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190- Inserm 1207), Marseille, France
| | - Laurence Thirion
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190- Inserm 1207), Marseille, France
| | - Pornsawan Leaungwutiwong
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Xavier de Lamballerie
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190- Inserm 1207), Marseille, France
| | - Dorothée Missé
- MIVEGEC, CNRS, IRD, Univ. Montpellier, Montpellier, France
| | - Sineewanlaya Wichit
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, Thailand.
- Viral Vector Joint Unit and Joint Laboratory, Mahidol University, Nakhon Pathom, Thailand.
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3
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Lind K, Mölsä M, Kalin-Mänttäri L, Hemmilä H, Voutilainen L, Nikkari S. Vacuum Oven Drying: A Cost-Effective Way of Producing Field-Deployable Reagents for In-house Real-Time PCR Methods. Mol Biotechnol 2023:10.1007/s12033-023-00999-2. [PMID: 38135831 DOI: 10.1007/s12033-023-00999-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023]
Abstract
The polymerase chain reaction (PCR), is a widely used, sensitive and reliable method for detecting pathogens. However, technical limitations may restrict its use outside sophisticated laboratories, e.g. for detecting pathogens at the site of a disease outbreak. In this study, real-time PCR reagents specific to four bacteria (Bacillus anthracis, Yersinia pestis, Francisella tularensis, and Brucella spp.) and to the Influenza A virus were dried using a vacuum oven drying method. The performance of the dried reagents stored at different temperatures, was monitored using both a standard-size and a portable real-time PCR instrument. The vacuum oven dried real-time PCR reagents were stable and retained the sensitivity for at least 14 months when stored in a refrigerator (+ 4 °C). When stored at room temperature, DNA assays remained stable for at least 10 weeks and Influenza A RNA assay for 3 weeks. These results demonstrate the feasibility of vacuum oven dried real-time PCR reagents and a portable thermocycler for the rapid and reliable detection of pathogens. The drying protocol presented here is cost-effective and easy to use, and could be applied to real-time PCR methods specific to other pathogens as well. In addition, this in-house drying protocol reduces reliance on commercial PCR tests during a time of shortage, such as that experienced during the Corovirus disease (COVID-19) crisis.
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Affiliation(s)
- Katja Lind
- Centre for Military Medicine, Finnish Defence Forces, P.O. Box 50, 00301, Helsinki, Finland.
- Finnish Institute for Health and Welfare, P.O. Box 30, 00271, Helsinki, Finland.
| | - Markos Mölsä
- Centre for Military Medicine, Finnish Defence Forces, P.O. Box 50, 00301, Helsinki, Finland
| | | | - Heidi Hemmilä
- Centre for Military Medicine, Finnish Defence Forces, P.O. Box 50, 00301, Helsinki, Finland
| | - Liina Voutilainen
- Finnish Institute for Health and Welfare, P.O. Box 30, 00271, Helsinki, Finland
| | - Simo Nikkari
- Centre for Military Medicine, Finnish Defence Forces, P.O. Box 50, 00301, Helsinki, Finland
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4
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Xu Y, Xu T, Chen S, Yao H, Chen Y, Zeng Y, Chen F, Zhang G. Evaluation of a novel lyophilized-pellet-based 2019-nCoV nucleic acid detection kit for the diagnosis of COVID-19. PLoS One 2023; 18:e0292902. [PMID: 37878570 PMCID: PMC10599558 DOI: 10.1371/journal.pone.0292902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 09/30/2023] [Indexed: 10/27/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has swept the world and poses a serious threat to human health. In the post-pandemic-era, we must remain vigilant against the co-infection of SARS-CoV-2 and other respiratory viruses. More accurate and convenient detection methods are required for the diagnosis of SARS-CoV-2 due to its prolonged existence. In this study, the application value of a novel lyophilized-pellet-based 2019-nCoV nucleic acid diagnostic kit (PCoV-Kit) was evaluated by comparing it with a conventional liquid diagnostic kit (LCoV-Kit). We assessed the sensitivity, precision, accuracy, specificity, and amplification efficiency of PCoV-Kit and LCoV-Kit using diluted SARS-CoV-2 RNA reference materials. The results showed that both kits had high sensitivity, precision, accuracy, and specificity. A total of 2,033 oropharyngeal swab specimens collected during mass screening in Fuzhou in December 2022 were applied for the consistency analysis of the two reagents. In the detection of clinical oropharyngeal swab specimens, although the positive rate of PCoV-Kit (19.28%) was slightly lower than that of LCoV-Kit (20.86%), statistical analysis demonstrated a high degree of consistency between the test results obtained using both kit (χ2 = 1.57, P>0.05; Kappa coefficient = 0.90, 95%CI: 0.88-0.93). In conclusion, the use of lyophilized PCoV-Kit provides a non-inferior assay for the diagnosis of COVID-19.
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Affiliation(s)
- Yiyuan Xu
- Research and Development Department, Fujian CapitalBio Medical laboratory, Fuzhou, Fujian, China
| | - Tian Xu
- Research and Development Department, Fujian CapitalBio Medical laboratory, Fuzhou, Fujian, China
| | - Shaoting Chen
- Clinical Laboratory, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Huakang Yao
- Medical Department, Fujian Provincial Yongtai County Hospital, Fuzhou, Fujian, China
| | - Yuxiang Chen
- Research and Development Department, Fujian CapitalBio Medical laboratory, Fuzhou, Fujian, China
| | - Yanfen Zeng
- Fujian Provincial Center for Clinical Laboratory, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Falin Chen
- Clinical Laboratory, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Guanbin Zhang
- Research and Development Department, Fujian CapitalBio Medical laboratory, Fuzhou, Fujian, China
- Research and Development Department, National Engineering Research Center for Beijing Biochip Technology, Beijing, China
- Department of Laboratory Medicine, Fujian Medical University, Fuzhou, Fujian, China
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5
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Elbadry MA, Efstathion CA, Qualls WA, Tagliamonte MS, Alam MM, Khan MSR, Ryan SJ, Xue RD, Charrel RN, Bangonan L, Salemi M, Ayhan N, Lednicky JA, Morris JG. Diversity and Genetic Reassortment of Keystone Virus in Mosquito Populations in Florida. Am J Trop Med Hyg 2023; 108:1256-1263. [PMID: 37127267 PMCID: PMC10540117 DOI: 10.4269/ajtmh.22-0594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 02/10/2023] [Indexed: 05/03/2023] Open
Abstract
Keystone orthobunyavirus (KEYV), a member of the genus Orthobunyavirus, was first isolated in 1964 from mosquitoes in Keystone, Florida. Although data on human infections are limited, the virus has been linked to a fever/rash syndrome and, possibly, encephalitis, with early studies suggesting that 20% of persons in the Tampa, Florida, region had antibodies to KEYV. To assess the distribution and diversity of KEYV in other regions of Florida, we collected > 6,000 mosquitoes from 43 sampling sites in St. Johns County between June 2019 and April 2020. Mosquitoes were separated into pools by species and collection date and site. All pools with Aedes spp. (293 pools, 2,171 mosquitoes) were screened with a real-time reverse transcriptase polymerase chain reaction (rRT-PCR) assay that identifies KEYV and other closely related virus species of what was previously designated as the California encephalitis serogroup. In 2020, screening for KEYV was expanded to include 211 pools of Culex mosquitoes from sites where KEYV-positive Aedes spp. had been identified. rRT-PCR-positive samples were inoculated into cell cultures, and five KEYV isolates from Aedes atlanticus pools were isolated and sequenced. Analyses of the KEYV large genome segment sequences revealed two distinct KEYV clades, whereas analyses of the medium and small genome segments uncovered past reassortment events. Our data documented the ongoing seasonal circulation of multiple KEYV clades within Ae. atlanticus mosquito populations along the east coast of Florida, highlighting the need for further studies of the impact of this virus on human health.
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Affiliation(s)
- Maha A. Elbadry
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida
| | | | | | - Massimiliano S. Tagliamonte
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, Florida
| | - Md. Mahbubul Alam
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida
| | - Md. Siddiqur Rahman Khan
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida
| | - Sadie J. Ryan
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida
- Department of Geography, College of Liberal Arts and Sciences, University of Florida, Gainesville, Florida
| | - Rui-de Xue
- Anastasia Mosquito Control District, St. Augustine, Florida
| | - Remi N. Charrel
- Unité des Virus Emergents, Aix Marseille University, INSERM U1207, Marseille, France
| | - Lea Bangonan
- Anastasia Mosquito Control District, St. Augustine, Florida
| | - Marco Salemi
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, Florida
| | - Nazli Ayhan
- Unité des Virus Emergents, Aix Marseille University, INSERM U1207, Marseille, France
| | - John A. Lednicky
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida
| | - J. Glenn Morris
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida
- Department of Medicine, College of Medicine, University of Florida, Gainesville, Florida
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Deng X, Li L, Cai X, Lin Y, Lan Y. Evaluation of the performance of a novel HIV-1 viral load assay for HIV quantification in China. HIV Med 2023. [PMID: 36843437 DOI: 10.1111/hiv.13473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 02/12/2023] [Indexed: 02/28/2023]
Abstract
OBJECTIVES Our objective was to assess the HIV-1 quantification performance of the Livzon HIV-1 viral load (VL) assay and the Roche Cobas HIV-1 assay to evaluate an HIV-1 VL testing reagent for application in China. METHOD We compared the Livzon and Roche Cobas HIV-1 VL assays using ethylenediaminetetraacetic acid plasma samples collected between May 2021 and November 2021 from patients with HIV-1 and healthy controls. We used Cohen's κ coefficient to measure agreement of qualitative values and Pearson's correlation coefficient (r) values and the coefficient of determination (R2 ) to determine the linear relationship between the two assays. We performed a Bland-Altman analysis to assess VL quantification agreement. RESULTS In total, 11 plasma samples from patients with hepatitis B virus (HBV) or hepatitis C virus (HCV) and nine samples from healthy controls were undetectable on both assays. Overall agreement was seen in 419 of 500 specimens (91.40%), with a κ value of 0.59. Pearson's correlation coefficient between the two assays was 0.970. Using the Bland-Altman method, 95.14% (352/370) of paired VLs fell within the 95% confidence limits of agreement (-0.51 to 0.95 log10 copies/mL). Higher VLs had a better correlation and a smaller mean difference between the two assays. Pearson's correlation coefficient for the samples of subtype CRF01_AE, CRF07_BC, and CRF55_01B was 0.950, 0.935, and 0.952, respectively. CONCLUSION The Livzon HIV-1 VL assay exhibits good precision and linearity and a high correlation with the Roche Cobas HIV-1 assay. The Livzon HIV-1 VL assay has salient advantages in terms of the lyophilized powder reagent, which gives the assay greater stability and sensitivity and can be readily used in low-resource areas.
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Affiliation(s)
- Xizi Deng
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Liya Li
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Xiaoli Cai
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yaqing Lin
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yun Lan
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
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7
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Genome Sequence of Genotype 1A Hepatovirus A Isolated from Plasma from a Haitian Child. Microbiol Resour Announc 2022; 11:e0044922. [PMID: 35950865 PMCID: PMC9476952 DOI: 10.1128/mra.00449-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genotype 1A hepatovirus A was identified by quantitative reverse transcription-PCR and isolated from plasma from a Haitian child with acute undifferentiated febrile illness and malaise. The strain was most closely related to Brazilian strains, consistent with recognized patterns of virus movement in the Caribbean region.
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Saba Villarroel PM, Castro Soto MDR, Melendres Flores O, Peralta Landívar A, Calderón ME, Loayza R, Boucraut J, Thirion L, Dubot-Pérès A, Ninove L, de Lamballerie X. A clinical, aetiological, and public health perspective on central nervous system infections in Bolivia, 2017-2018. Sci Rep 2021; 11:23235. [PMID: 34853372 PMCID: PMC8636643 DOI: 10.1038/s41598-021-02592-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 11/16/2021] [Indexed: 11/10/2022] Open
Abstract
Central nervous system (CNS) infections are important causes of morbidity and mortality worldwide. In Bolivia, aetiologies, case fatality, and determinants of outcome are poorly characterised. We attempted to investigate such parameters to guide diagnosis, treatment, prevention, and health policy. From Nov-2017 to Oct-2018, we prospectively enrolled 257 inpatients (20.2% HIV-positive patients) of all ages from healthcare centers of Cochabamba and Santa Cruz, Bolivia with a suspected CNS infection and a lumbar puncture performed. Biological diagnosis included classical microbiology, molecular, serological and immunohistochemical tests. An infectious aetiology was confirmed in 128/257 (49.8%) inpatients, including, notably among confirmed single and co-infections, Cryptococcus spp. (41.7%) and Mycobacterium tuberculosis (27.8%) in HIV-positive patients, and Mycobacterium tuberculosis (26.1%) and Streptococcus pneumoniae (18.5%) in HIV-negative patients. The total mortality rate was high (94/223, 42.1%), including six rabies cases. In multivariate logistic regression analysis, mortality was associated with thrombocytopenia (Odds ratio (OR) 5.40, 95%-CI 2.40-11.83) and hydrocephalus (OR 4.07, 95%-CI 1.35-12.23). The proportion of untreated HIV patients, late presentations of neurotuberculosis, the rate of pneumococcal cases, and rabies patients who did not benefit from a post-exposure prophylaxis, suggest that decreasing the burden of CNS infections requires reinforcing health policy regarding tuberculosis, rabies, S. pneumoniae vaccination, and HIV-infections.
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Affiliation(s)
- Paola Mariela Saba Villarroel
- Unité des Virus Émergents (UVE: Aix-Marseille Univ.-IRD 190-INSERM 1207-IHU Méditerranée Infection), 13005, Marseille, France.
- Molecular Biology Unit, Centro Nacional de Enfermedades Tropicales (CENETROP), Santa Cruz de la Sierra, Bolivia.
| | | | | | | | - María E Calderón
- Infectology Department, Manuel Ascencio Villarroel Hospital, Cochabamba, Bolivia
| | - Roxana Loayza
- Molecular Biology Unit, Centro Nacional de Enfermedades Tropicales (CENETROP), Santa Cruz de la Sierra, Bolivia
| | - José Boucraut
- Immunology Laboratory, Conception Hospital, 13005, Marseille, France
- Timone Neuroscience Institute, Aix-Marseille University, 13005, Marseille, France
| | - Laurence Thirion
- Unité des Virus Émergents (UVE: Aix-Marseille Univ.-IRD 190-INSERM 1207-IHU Méditerranée Infection), 13005, Marseille, France
| | - Audrey Dubot-Pérès
- Unité des Virus Émergents (UVE: Aix-Marseille Univ.-IRD 190-INSERM 1207-IHU Méditerranée Infection), 13005, Marseille, France
| | - Laetitia Ninove
- Unité des Virus Émergents (UVE: Aix-Marseille Univ.-IRD 190-INSERM 1207-IHU Méditerranée Infection), 13005, Marseille, France
| | - Xavier de Lamballerie
- Unité des Virus Émergents (UVE: Aix-Marseille Univ.-IRD 190-INSERM 1207-IHU Méditerranée Infection), 13005, Marseille, France
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9
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Xu J, Wang J, Su X, Qiu G, Zhong Q, Li T, Zhang D, Zhang S, He S, Ge S, Zhang J, Xia N. Transferable, easy-to-use and room-temperature-storable PCR mixes for microfluidic molecular diagnostics. Talanta 2021; 235:122797. [PMID: 34517655 PMCID: PMC8353973 DOI: 10.1016/j.talanta.2021.122797] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 08/04/2021] [Accepted: 08/07/2021] [Indexed: 10/26/2022]
Abstract
As the outbreak of coronavirus disease 2019 (COVID-19), on-site molecular diagnosis is becoming increasingly important. In this study, a freeze-drying method was introduced for PCR reagents to meet the requirements of microfluidic molecular diagnosis. Using this method, PCR components were pre-mixed and freeze-dried as a bead, which could be transferred into microfluidic chips easily. As this bead only required reconstitution in water, operational steps of PCR were simplified, pipetting errors and errors associated with improper handling of wet reagents could also be reduced. In addition, 19 PCR mixes for different targets (including both RNA and DNA) detection were stable when stored at room temperature (18-25 °C) for 1-2 years and may be stored longer as activity monitoring remains ongoing. To shorten the stability testing time, accelerated stability testing at higher temperatures was proposed. The evaluation periods of the freeze-dried PCR mixes were shortened to less than one month when stored at 56 °C and 80 °C. When attempts were further tried to predict the shelf lives for freeze-dried PCR mixes, our findings challenged the classic view of the Q10 method as a prediction model for freeze-dried PCR mixes and confirmed for the first time that this prediction was influenced by different factors at varying degrees. These studies and findings are important for the development of molecular diagnosis at both central laboratories and resource-limited areas.
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Affiliation(s)
- Jiasu Xu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Jin Wang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, 361102, China; School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Xiaosong Su
- Xiang'an Hospital of Xiamen University, Xiamen, 361102, China
| | - Guofu Qiu
- Xiamen Innovax Biotech CO., LTD., Xiamen, 361022, China
| | | | - Tingdong Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Dongxu Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Shiyin Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, 361102, China.
| | - Shuizhen He
- Haicang Hospital of Xiamen, Xiamen, 361026, China.
| | - Shengxiang Ge
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Jun Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Ningshao Xia
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, 361102, China; School of Life Sciences, Xiamen University, Xiamen, 361102, China
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10
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Hammerling MJ, Warfel KF, Jewett MC. Lyophilization of premixed COVID-19 diagnostic RT-qPCR reactions enables stable long-term storage at elevated temperature. Biotechnol J 2021; 16:e2000572. [PMID: 33964860 PMCID: PMC8237061 DOI: 10.1002/biot.202000572] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/29/2021] [Accepted: 04/30/2021] [Indexed: 12/15/2022]
Abstract
Reverse transcriptase‐quantitative polymerase chain reaction (RT‐qPCR) diagnostic tests for SARS‐CoV‐2 are the cornerstone of the global testing infrastructure. However, these tests require cold‐chain shipping to distribute, and the labor of skilled technicians to assemble reactions and interpret the results. Strategies to reduce shipping and labor costs at the point‐of‐care could aid in diagnostic testing scale‐up and response to the COVID‐19 outbreak, as well as in future outbreaks.
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Affiliation(s)
- Michael J Hammerling
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
| | - Katherine F Warfel
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA.,Center for Synthetic Biology, Northwestern University, Evanston, Illinois, USA.,Simpson Querrey Institute, Northwestern University, Evanston, Illinois, USA.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, Illinois, USA
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11
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Yang S, Wen W. Lyophilized Ready-to-Use Mix for the Real-Time Polymerase Chain Reaction Diagnosis. ACS APPLIED BIO MATERIALS 2021; 4:4354-4360. [PMID: 35006847 DOI: 10.1021/acsabm.1c00131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Real-time polymerase chain reaction (real-time PCR) brings a more efficient and accurate method for detecting and analyzing nucleic acids in hospitals and laboratories. To solve the inconvenience of PCR reagent delivery and storage via cold-chain transportation, a solid-state reagent with robust characteristics should be employed. In this report, a lyophilized mix containing all necessary components for real-time PCR and its production method was designed, and its stability was tested at different temperatures. Some cryoprotectants and carriers are required to protect the function of the enzyme and primer as much as possible and provide the cake structure. Formulations with polyhydroxy compounds were considered to have the potential for protecting the enzymatic microstructure and functionality of dried mixes during the whole manufacturing and cold-free storage. The final products with the most superior protective formulation containing trehalose, Ficoll 400, and gelatin were able to provide the totally same testing result and sensitivity as the freshly made mix after 300 days of storage at 45 °C and can be deduced to maintain the function at room temperature (22.5-25.5 °C) for about 2 years.
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Affiliation(s)
- Siyu Yang
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon 999077, Hong Kong
| | - Weijia Wen
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon 999077, Hong Kong
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12
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Loveday EK, Zath GK, Bikos DA, Jay ZJ, Chang CB. Screening of Additive Formulations Enables Off-Chip Drop Reverse Transcription Quantitative Polymerase Chain Reaction of Single Influenza A Virus Genomes. Anal Chem 2021; 93:4365-4373. [PMID: 33635052 PMCID: PMC10016143 DOI: 10.1021/acs.analchem.0c03455] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The miniaturization of polymerase chain reaction (PCR) using drop-based microfluidics allows for amplification of single nucleic acids in aqueous picoliter-sized drops. Accurate data collection during PCR requires that drops remain stable to coalescence during thermocycling and drop contents are retained. Following systematic testing of known PCR additives, we identified an optimized formulation of 1% w/v Tween-20, 0.8 μg/μL bovine serum albumin, 1 M betaine in the aqueous phase, and 3 wt % (w/w) of the polyethylene glycol-perfluoropolyether2 surfactant in the oil phase of 50 μm diameter drops that maintains drop stability and prevents dye transport. This formulation enables a method we call off-chip drop reverse transcription quantitative PCR (OCD RT-qPCR) in which drops are thermocycled in a qPCR machine and sampled at various cycle numbers "off-chip", or outside of a microfluidic chip. qPCR amplification curves constructed from hundreds of individual drops using OCD RT-qPCR and imaged using epifluorescence microscopy correlate with amplification curves of ≈300,000 drops thermocycled using a qPCR machine. To demonstrate the utility of OCD RT-qPCR, influenza A virus (IAV) RNA was detected down to a single viral genome copy per drop, or 0.320 cpd. This work was extended to perform multiplexed detection of IAV M gene RNA and cellular β-actin DNA in drops, and direct amplification of IAV genomes from infected cells without a separate RNA extraction step. The optimized additive formulation and the OCD-qPCR method allow for drop-based RT-qPCR without complex devices and demonstrate the ability to quantify individual or rare nucleic acid species within drops with minimal processing.
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Affiliation(s)
- Emma Kate Loveday
- Center for Biofilm Engineering and the Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana 59717, United States
| | - Geoffrey K Zath
- Center for Biofilm Engineering and the Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana 59717, United States
| | - Dimitri A Bikos
- Center for Biofilm Engineering and the Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana 59717, United States
| | - Zackary J Jay
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Connie B Chang
- Center for Biofilm Engineering and the Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana 59717, United States
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13
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Thirion L, Pezzi L, Pedrosa-Corral I, Sanbonmatsu-Gamez S, Lamballerie XD, Falchi A, Perez-Ruiz M, Charrel RN. Evaluation of a Trio Toscana Virus Real-Time RT-PCR Assay Targeting Three Genomic Regions within Nucleoprotein Gene. Pathogens 2021; 10:pathogens10030254. [PMID: 33668339 PMCID: PMC7996202 DOI: 10.3390/pathogens10030254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 02/01/2021] [Accepted: 02/16/2021] [Indexed: 12/30/2022] Open
Abstract
Toscana virus (TOSV) can cause central nervous system infections in both residents of and travelers to Mediterranean countries. Data mining identified three real-time RT-qPCR assays for detecting TOSV RNA targeting non-overlapping regions in the nucleoprotein gene. Here, they were combined to create a multi-region assay named Trio TOSV RT-qPCR consisting of six primers and three probes. In this study, (i) we evaluated in silico the three RT-qPCR assays available in the literature for TOSV detection, (ii) we combined the three systems to create the Trio TOSV RT-qPCR, (iii) we assessed the specificity and sensitivity of the three monoplex assays versus the Trio TOSV RT-qPCR assay, and (iv) we compared the performance of the Trio TOSV RT-qPCR assay with one of the reference monoplex assays on clinical samples. In conclusion, the Trio TOSV RT-qPCR assay performs equally or better than the three monoplex assays; therefore, it provides a robust assay that can be used for both research and diagnostic purposes.
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Affiliation(s)
- Laurence Thirion
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207-IHU Méditerranée Infection), 13005 Marseille, France; (L.T.); (L.P.); (X.D.L.)
| | - Laura Pezzi
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207-IHU Méditerranée Infection), 13005 Marseille, France; (L.T.); (L.P.); (X.D.L.)
- UR7310, Laboratoire de Virologie, Université de Corse-Inserm, 20250 Corte, France;
| | - Irene Pedrosa-Corral
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Instituto de Investigación Biosanitaria ibs.Granada, 18014 Granada, Spain; (I.P.-C.); (S.S.-G.); (M.P.-R.)
| | - Sara Sanbonmatsu-Gamez
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Instituto de Investigación Biosanitaria ibs.Granada, 18014 Granada, Spain; (I.P.-C.); (S.S.-G.); (M.P.-R.)
| | - Xavier De Lamballerie
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207-IHU Méditerranée Infection), 13005 Marseille, France; (L.T.); (L.P.); (X.D.L.)
| | - Alessandra Falchi
- UR7310, Laboratoire de Virologie, Université de Corse-Inserm, 20250 Corte, France;
| | - Mercedes Perez-Ruiz
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Instituto de Investigación Biosanitaria ibs.Granada, 18014 Granada, Spain; (I.P.-C.); (S.S.-G.); (M.P.-R.)
| | - Remi N. Charrel
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207-IHU Méditerranée Infection), 13005 Marseille, France; (L.T.); (L.P.); (X.D.L.)
- Correspondence:
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14
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Pezzi L, Charrel RN, Ninove L, Nougairede A, Molle G, Coutard B, Durand G, Leparc-Goffart I, de Lamballerie X, Thirion L. Development and Evaluation of a duo SARS-CoV-2 RT-qPCR Assay Combining Two Assays Approved by the World Health Organization Targeting the Envelope and the RNA-Dependant RNA Polymerase (RdRp) Coding Regions. Viruses 2020; 12:E686. [PMID: 32630601 PMCID: PMC7354606 DOI: 10.3390/v12060686] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/05/2020] [Accepted: 06/24/2020] [Indexed: 12/12/2022] Open
Abstract
The recent emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) worldwide has highlighted the importance of reliable and rapid diagnostic testing to prevent and control virus circulation. Dozens of monoplex in-house RT-qPCR assays are already available; however, the development of dual-target assays is suited to avoid false-negative results caused by polymorphisms or point mutations, that can compromise the accuracy of diagnostic and screening tests. In this study, two mono-target assays recommended by WHO (E-Sarbeco (enveloppe gene, Charite University, Berlin, Germany) and RdRp-IP4 (RdRp, Institut Pasteur, Paris, France)) were selected and combined in a unique robust test; the resulting duo SARS-CoV-2 RT-qPCR assay was compared to the two parental monoplex tests. The duo SARS-CoV-2 assay performed equally, or better, in terms of sensitivity, specificity, linearity and signal intensity. We demonstrated that combining two single systems into a dual-target assay (with or without an MS2-based internal control) did not impair performances, providing a potent tool adapted for routine molecular diagnosis in clinical microbiology laboratories.
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Affiliation(s)
- Laura Pezzi
- UR7310, Laboratoire de Virologie, Université de Corse-Inserm, 20250 Corte, France;
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207-IHU Méditerranée Infection), 13005 Marseille, France; (L.N.); (A.N.); (G.M.); (B.C.); (G.D.); (I.L.-G.); (X.d.L.); (L.T.)
| | - Remi N. Charrel
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207-IHU Méditerranée Infection), 13005 Marseille, France; (L.N.); (A.N.); (G.M.); (B.C.); (G.D.); (I.L.-G.); (X.d.L.); (L.T.)
| | - Laetitia Ninove
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207-IHU Méditerranée Infection), 13005 Marseille, France; (L.N.); (A.N.); (G.M.); (B.C.); (G.D.); (I.L.-G.); (X.d.L.); (L.T.)
| | - Antoine Nougairede
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207-IHU Méditerranée Infection), 13005 Marseille, France; (L.N.); (A.N.); (G.M.); (B.C.); (G.D.); (I.L.-G.); (X.d.L.); (L.T.)
| | - Gregory Molle
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207-IHU Méditerranée Infection), 13005 Marseille, France; (L.N.); (A.N.); (G.M.); (B.C.); (G.D.); (I.L.-G.); (X.d.L.); (L.T.)
| | - Bruno Coutard
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207-IHU Méditerranée Infection), 13005 Marseille, France; (L.N.); (A.N.); (G.M.); (B.C.); (G.D.); (I.L.-G.); (X.d.L.); (L.T.)
| | - Guillaume Durand
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207-IHU Méditerranée Infection), 13005 Marseille, France; (L.N.); (A.N.); (G.M.); (B.C.); (G.D.); (I.L.-G.); (X.d.L.); (L.T.)
- Institut de Recherche Biomédicale des Armées, National Reference Laboratory for Arboviruses, 13005 Marseille, France
| | - Isabelle Leparc-Goffart
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207-IHU Méditerranée Infection), 13005 Marseille, France; (L.N.); (A.N.); (G.M.); (B.C.); (G.D.); (I.L.-G.); (X.d.L.); (L.T.)
- Institut de Recherche Biomédicale des Armées, National Reference Laboratory for Arboviruses, 13005 Marseille, France
| | - Xavier de Lamballerie
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207-IHU Méditerranée Infection), 13005 Marseille, France; (L.N.); (A.N.); (G.M.); (B.C.); (G.D.); (I.L.-G.); (X.d.L.); (L.T.)
| | - Laurence Thirion
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207-IHU Méditerranée Infection), 13005 Marseille, France; (L.N.); (A.N.); (G.M.); (B.C.); (G.D.); (I.L.-G.); (X.d.L.); (L.T.)
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